The quest for orthologs: finding the corresponding gene across genomes
Orthology is a key evolutionary concept in many areas of genomic research. It provides a
framework for subjects as diverse as the evolution of genomes, gene functions, cellular …
framework for subjects as diverse as the evolution of genomes, gene functions, cellular …
Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database
Abstract The Pseudomonas Genome Database (http://www. pseudomonas. com) is well
known for the application of community-based annotation approaches for producing a high …
known for the application of community-based annotation approaches for producing a high …
Inferring orthology and paralogy
The distinction between orthologs and paralogs, genes that started diverging by speciation
versus duplication, is relevant in a wide range of contexts, most notably phylogenetic tree …
versus duplication, is relevant in a wide range of contexts, most notably phylogenetic tree …
InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation
Abstract InnateDB (http://www. innatedb. com) is an integrated analysis platform that has
been specifically designed to facilitate systems-level analyses of mammalian innate …
been specifically designed to facilitate systems-level analyses of mammalian innate …
Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes
GL Winsor, DKW Lam, L Fleming, R Lo… - Nucleic acids …, 2010 - academic.oup.com
Pseudomonas is a metabolically-diverse genus of bacteria known for its flexibility and
leading free living to pathogenic lifestyles in a wide range of hosts. The Pseudomonas …
leading free living to pathogenic lifestyles in a wide range of hosts. The Pseudomonas …
Choosing BLAST options for better detection of orthologs as reciprocal best hits
G Moreno-Hagelsieb, K Latimer - Bioinformatics, 2008 - academic.oup.com
Motivation: The analyses of the increasing number of genome sequences requires shortcuts
for the detection of orthologs, such as Reciprocal Best Hits (RBH), where orthologs are …
for the detection of orthologs, such as Reciprocal Best Hits (RBH), where orthologs are …
Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa
Pseudomonas aeruginosa isolates have a highly conserved core genome representing up
to 90% of the total genomic sequence with additional variable accessory genes, many of …
to 90% of the total genomic sequence with additional variable accessory genes, many of …
InnateDB: facilitating systems‐level analyses of the mammalian innate immune response
Although considerable progress has been made in dissecting the signaling pathways
involved in the innate immune response, it is now apparent that this response can no longer …
involved in the innate immune response, it is now apparent that this response can no longer …
Computational methods for Gene Orthology inference
Accurate inference of orthologous genes is a pre-requisite for most comparative genomics
studies, and is also important for functional annotation of new genomes. Identification of …
studies, and is also important for functional annotation of new genomes. Identification of …
The Burkholderia Genome Database: facilitating flexible queries and comparative analyses
As the genome sequences of multiple strains of a given bacterial species are obtained, more
generalized bacterial genome databases may be complemented by databases that are …
generalized bacterial genome databases may be complemented by databases that are …